ALPL c.69_74del
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
hypophosphatasia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.58 | GERP -0.75, phastCons 0.092 |
| Non-coding constraint | Z 1.23 | 1 kb window · o/e 0.90 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- ALPL
- Coding
- c.69_74del
- MANE Select
- NM_000478
- dbSNP
- rs2148150789
- Type
- Microsatellite
- Location
- chr1:21560624 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.74 · 5 PDB
Disease context
hypophosphatasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hypophosphatasia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- All ages
Similar variants
- ALPL p.Ala498fs Likely pathogenic ★★ same condition
- ALPL p.His79fs Likely pathogenic ★★ same condition
- ALPL p.Leu372fs Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Phe328del Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Ser310fs Pathogenic ★★ same condition
- ALPL p.Ser364fs Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Ser368del Pathogenic ★★ same condition
- ALPL p.Ser394fs Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/alpl-c-69-74del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown